Ingest and query genomic intervals from multiple BED files

Overview

Region search with tileDB

Ingest and query genomic intervals from multiple BED files.

Ingest

>>> import glob
>>> import tiles
# Get paths to local BED files.
>>> files = sorted(glob.glob('/path/to/beds/*.bed.gz'))
>>> files[:5]
[
    'ENCFF001SOF.bed.gz',
    'ENCFF001SOH.bed.gz',
    'ENCFF001SOM.bed.gz',
    'ENCFF001SON.bed.gz',
    'ENCFF001SOO.bed.gz',
]
# Create chromosome by genomic position database.
>>> tiles.create_region_array('regions')
# Load first five BEDs into tileDB.
>>> tiles.load_local('regions', files[:5])
...
generating positions
writing data
done
...
# Save accession to file index maps.
>>> tiles.save_maps('regions')
# Consolidate and vacuum database.
>>> tiles.clean('regions')

Query

>>> import tiles
# Load accession to file index maps.
>> tiles.load_maps('regions')
# Get first five intervals around POMC gene on chromosome two.
>>> tiles.query_region('regions', 2, 25132492, 25192278, limit=5)
[
    ('ENCFF001SOF.bed.gz', 25139665, 25139815),
    ('ENCFF001SOF.bed.gz', 25141485, 25141635),
    ('ENCFF001SOF.bed.gz', 25141625, 25141775),
    ('ENCFF001SOF.bed.gz', 25142065, 25142215),
    ('ENCFF001SOF.bed.gz', 25142665, 25142815),
]
# Get total number of intervals in that region.
>>> len(tiles.query_region('regions', 2, 25132492, 25192278, limit=1000))
52
# Get files with intervals in that region.
>>> tiles.query_file('regions', 2, 25132492, 25192278)
[
    'ENCFF001SOF.bed.gz',
    'ENCFF001SOH.bed.gz',
    'ENCFF001SOM.bed.gz',
]
Implemented a Google Maps prototype that provides the shortest route in terms of distance

Implemented a Google Maps prototype that provides the shortest route in terms of distance, the fastest route, the route with the fewest turns, and a scenic route that avoids roads when provided a sou

1 Dec 26, 2021
Minimum Bounding Box of Geospatial data

BBOX Problem definition: The spatial data users often are required to obtain the coordinates of the minimum bounding box of vector and raster data in

Ali Khosravi Kazazi 1 Sep 08, 2022
List of Land Cover datasets in the GEE Catalog

List of Land Cover datasets in the GEE Catalog A list of all the Land Cover (or discrete) datasets in Google Earth Engine. Values, Colors and Descript

David Montero Loaiza 5 Aug 24, 2022
Tools for the extraction of OpenStreetMap street network data

OSMnet Tools for the extraction of OpenStreetMap (OSM) street network data. Intended to be used in tandem with Pandana and UrbanAccess libraries to ex

Urban Data Science Toolkit 47 Sep 21, 2022
framework for large-scale SAR satellite data processing

pyroSAR A Python Framework for Large-Scale SAR Satellite Data Processing The pyroSAR package aims at providing a complete solution for the scalable or

John Truckenbrodt 389 Dec 21, 2022
Yet Another Time Series Model

Yet Another Timeseries Model (YATSM) master v0.6.x-maintenance Build Coverage Docs DOI | About Yet Another Timeseries Model (YATSM) is a Python packag

Chris Holden 60 Sep 13, 2022
r.cfdtools 7 Dec 28, 2022
An API built to format given addresses using Python and Flask.

An API built to format given addresses using Python and Flask. About The API returns properly formatted data, i.e. removing duplicate fields, distingu

1 Feb 27, 2022
Get Landsat surface reflectance time-series from google earth engine

geextract Google Earth Engine data extraction tool. Quickly obtain Landsat multispectral time-series for exploratory analysis and algorithm testing On

Loïc Dutrieux 50 Dec 15, 2022
Streamlit Component for rendering Folium maps

streamlit-folium This Streamlit Component is a work-in-progress to determine what functionality is desirable for a Folium and Streamlit integration. C

Randy Zwitch 224 Dec 30, 2022
This is a simple python code to get IP address and its location using python

IP address & Location finder @DEV/ED : Pavan Ananth Sharma Dependencies: ip2geotools Note: use pip install ip2geotools to install this in your termin

Pavan Ananth Sharma 2 Jul 05, 2022
🌐 Local tile server for viewing geospatial raster files with ipyleaflet or folium

🌐 Local Tile Server for Geospatial Rasters Need to visualize a rather large (gigabytes) raster you have locally? This is for you. A Flask application

Bane Sullivan 192 Jan 04, 2023
A ready-to-use curated list of Spectral Indices for Remote Sensing applications.

A ready-to-use curated list of Spectral Indices for Remote Sensing applications. GitHub: https://github.com/davemlz/awesome-ee-spectral-indices Docume

David Montero Loaiza 488 Jan 03, 2023
Python module to access the OpenCage geocoding API

OpenCage Geocoding Module for Python A Python module to access the OpenCage Geocoder. Build Status / Code Quality / etc Usage Supports Python 3.6 or n

OpenCage GmbH 57 Nov 01, 2022
Xarray backend to Copernicus Sentinel-1 satellite data products

xarray-sentinel WARNING: this product is a "technology preview" / pre-Alpha Xarray backend to explore and load Copernicus Sentinel-1 satellite data pr

B-Open 191 Dec 15, 2022
A toolbox for processing earth observation data with Python.

eo-box eobox is a Python package with a small collection of tools for working with Remote Sensing / Earth Observation data. Package Overview So far, t

13 Jan 06, 2022
Centroids as a Service

Centroids! This application reads a valid geojson FeatureCollection and returns a valid geojson FeatureColleciton of centroids. In the output: All pro

Lyzi Diamond 20 Aug 29, 2021
Constraint-based geometry sketcher for blender

Geometry Sketcher Constraint-based sketcher addon for Blender that allows to create precise 2d shapes by defining a set of geometric constraints like

1.7k Jan 02, 2023
Record railway train route profile with GNSS tools

Train route profile recording with GNSS technology based on ARDUINO platform Project target Develop GNSS recording tools based on the ARDUINO platform

tomcom 1 Jan 01, 2022
ESMAC diags - Earth System Model Aerosol-Cloud Diagnostics Package

Earth System Model Aerosol-Cloud Diagnostics Package This Earth System Model (ES

Pacific Northwest National Laboratory 1 Jan 04, 2022